X-80022027-TACAC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001109878.2(TBX22):c.-2-203_-2-200del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (459 hom., 2231 hem., cov: 0)
• Consequence: TBX22 NM_001109878.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.750

Genes affected

TBX22 (HGNC:11600): (T-box transcription factor 22) This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. Mutations in this gene have been associated with the inherited X-linked disorder, Cleft palate with ankyloglossia, and it is believed to play a major role in human palatogenesis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-80022027-TACAC-T is Benign according to our data. Variant chrX-80022027-TACAC-T is described in ClinVar as [Benign]. Clinvar id is 1236479.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX22	NM_001109878.2	c.-2-203_-2-200del		intron_variant		ENST00000373296.8
TBX22	NM_001109879.2	c.-358-203_-358-200del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX22	ENST00000373296.8	c.-2-203_-2-200del		intron_variant		5	NM_001109878.2	P1
TBX22	ENST00000626498.2	c.-2-203_-2-200del		intron_variant, NMD_transcript_variant		2
TBX22	ENST00000476373.1	n.120-203_120-200del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 10581 AN: 92812 Hom.: 459 Cov.: 0 AF XY: 0.112 AC XY: 2233 AN XY: 19996

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0172

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0755

Gnomad SAS AF: 0.0915

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0984

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.114 AC: 10577 AN: 92829 Hom.: 459 Cov.: 0 AF XY: 0.111 AC XY: 2231 AN XY: 20023

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0803

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0758

Gnomad4 SAS AF: 0.0901

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0971

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs200577659; hg19: chrX-79277526;